Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:3902077 original size:14 final size:14
Alignment explanation
Indices: 3902057--3902095 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3902047 CTTTTTATTT
3902057 ATTTCATTTCTATTC
1 ATTTCATTTCT-TTC
3902072 -TTTCATTTCTTTC
1 ATTTCATTTCTTTC
3902085 TATTTCATTTC
1 -ATTTCATTTC
3902096 CTTTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 10 0.45
15 9 0.41
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTCATTTCTTTC
Found at i:3902960 original size:7 final size:6
Alignment explanation
Indices: 3902943--3903007 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
3902933 GTGCAAAAAG
* ** *
3902943 AAAGAA AAAGACA AAAG-A AGAGAA AAATCA GAAG-A AAAG-A AAAGAA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
3902989 AAAGAA AAAGAA AAA-AA AA
1 AAAGAA AAAGAA AAAGAA AA
3903008 GTAAGCCAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
5 17 0.35
6 27 0.55
7 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:3902960 original size:17 final size:16
Alignment explanation
Indices: 3902937--3903008 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 16
3902927 ATTGGAGTGC
3902937 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
3902953 ACAAAAGAAGAGAAAAATCAG
1 A-AAAAGAA-AG-AAAA--AG
3902974 AAGAAAAGAAAAGAAAAAG
1 -A-AAAAG-AAAGAAAAAG
*
3902993 AAAAAGAAAAAAAAAG
1 AAAAAGAAAGAAAAAG
3903009 TAAGCCAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
16 10 0.21
17 12 0.26
18 3 0.06
19 6 0.13
21 6 0.13
22 8 0.17
23 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:3902966 original size:22 final size:21
Alignment explanation
Indices: 3902941--3903000 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
3902931 GAGTGCAAAA
3902941 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAGA-AAAAGAAG
** *
3902963 AGAAA-AATCAGAAGAA-AAG
1 AGAAAGAAAAAGAAAAAGAAG
3902982 A-AAAGAAAAAGAAAAAGAA
1 AGAAAGAAAAAGAAAAAGAA
3903001 AAAAAAAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 5 0.17
21 5 0.17
22 5 0.17
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAAAGAAAAAGAAG
Found at i:3903001 original size:22 final size:22
Alignment explanation
Indices: 3902943--3903008 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
3902933 GTGCAAAAAG
*
3902943 AAAGAAAAAGACAAAAGAAGAGAA
1 AAAGAAAAAG--AAAAGAAAAGAA
** *
3902967 AAATCAGAAGAAAAGAAAAGAA
1 AAAGAAAAAGAAAAGAAAAGAA
*
3902989 AAAGAAAAAGAAAAAAAAAG
1 AAAGAAAAAGAAAAGAAAAG
3903009 TAAGCCAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 27 0.79
24 7 0.21
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAGAAAAGAAAAGAA
Found at i:3911641 original size:19 final size:19
Alignment explanation
Indices: 3911619--3911660 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3911609 TTTTTTGAAA
*
3911619 TTTTGGCTTTTTTGGCTTT
1 TTTTGGCTTTTTTGCCTTT
* *
3911638 TTTTTGTTTTTTTGCCTTT
1 TTTTGGCTTTTTTGCCTTT
3911657 TTTT
1 TTTT
3911661 TGGGAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.14, T:0.76
Consensus pattern (19 bp):
TTTTGGCTTTTTTGCCTTT
Found at i:3911661 original size:19 final size:19
Alignment explanation
Indices: 3911626--3911662 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3911616 AAATTTTGGC
*
3911626 TTTTTTGGCTTTTTTTTGT
1 TTTTTTGCCTTTTTTTTGT
3911645 TTTTTTGCCTTTTTTTTG
1 TTTTTTGCCTTTTTTTTG
3911663 GGAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (19 bp):
TTTTTTGCCTTTTTTTTGT
Found at i:3913865 original size:19 final size:21
Alignment explanation
Indices: 3913824--3913873 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
3913814 TGATCACATC
3913824 AAAATACATGATTTTTAAATG
1 AAAATACATGATTTTTAAATG
3913845 AAAATACATGA-TTTT-AATG
1 AAAATACATGATTTTTAAATG
*
3913864 AAGATACATG
1 AAAATACATG
3913874 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (21 bp):
AAAATACATGATTTTTAAATG
Found at i:3914792 original size:30 final size:31
Alignment explanation
Indices: 3914751--3914812 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
3914741 ACATATTGCC
**
3914751 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
3914782 ATGA-ATCTAAAACATATGTAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
3914812 A
1 A
3914813 AAGCTAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:3915106 original size:24 final size:21
Alignment explanation
Indices: 3915072--3915114 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3915062 TGCACAAGAT
*
3915072 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
3915094 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
3915115 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:3920111 original size:28 final size:26
Alignment explanation
Indices: 3920058--3920114 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
3920048 TTCTTTGCTT
*
3920058 TTTCTTCTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGAGTGCTGGAATTTC
**
3920084 TTTCTTTCTTTTGGAGTGCTTTAATTTC
1 TTTC-TTCTTTT-GAGTGCTGGAATTTC
3920112 TTT
1 TTT
3920115 TTTGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 15 0.58
ACGTcount: A:0.09, C:0.14, G:0.16, T:0.61
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTGGAATTTC
Found at i:3928245 original size:24 final size:21
Alignment explanation
Indices: 3928211--3928253 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3928201 TGCACAAGAT
*
3928211 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
3928233 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
3928254 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:3929926 original size:24 final size:24
Alignment explanation
Indices: 3929899--3929956 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
3929889 CGCCTAAGAA
*
3929899 GAAGCGCATGACCAGCCATCATCC
1 GAAGCACATGACCAGCCATCATCC
3929923 GAAGCACATGACCAGCCATCATCC
1 GAAGCACATGACCAGCCATCATCC
3929947 -AATGCACATG
1 GAA-GCACATG
3929957 GGTGCACCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.33, C:0.34, G:0.19, T:0.14
Consensus pattern (24 bp):
GAAGCACATGACCAGCCATCATCC
Found at i:3931503 original size:11 final size:11
Alignment explanation
Indices: 3931472--3931531 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 11
3931462 TTGGAGTGCA
*
3931472 AAAAGAAAGA-
1 AAAAGAAAAAG
3931482 AAAAGACAAAAG
1 AAAAGA-AAAAG
*
3931494 AAGAGAAAAATCAG
1 AAAAG-AAAA--AG
3931508 AAAAGAAAAAG
1 AAAAGAAAAAG
3931519 AAAAG-AAAAG
1 AAAAGAAAAAG
3931529 AAA
1 AAA
3931532 TTCAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
10 14 0.33
11 10 0.24
12 7 0.17
13 5 0.12
14 6 0.14
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:3931525 original size:16 final size:16
Alignment explanation
Indices: 3931472--3931531 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
3931462 TTGGAGTGCA
3931472 AAAAG-AAAGAAAAAG
1 AAAAGAAAAGAAAAAG
*
3931487 ACAAA-AGAAGAGAAAA-
1 A-AAAGAAAAGA-AAAAG
**
3931503 ATCAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
3931519 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
3931532 TTCAAAAGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
15 6 0.18
16 24 0.71
17 4 0.12
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:3933597 original size:34 final size:34
Alignment explanation
Indices: 3933554--3933678 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
3933544 TTCGTCCTAC
*
3933554 TAGGATTCAAACTCCTAAAAATGGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
3933588 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
3933623 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
3933652 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
3933679 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 38 0.52
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:3934000 original size:24 final size:23
Alignment explanation
Indices: 3933957--3934002 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3933947 CATGTAATAT
*
3933957 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
3933980 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
3934003 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:3934088 original size:42 final size:42
Alignment explanation
Indices: 3933997--3934143 Score: 158
Period size: 44 Copynumber: 3.5 Consensus size: 42
3933987 CTTTAGTATA
* * * *
3933997 TATTTTTATTTTTTTAGA-TTATATATATAAATATATTATTTTT
1 TATTATTATTTTATTA-ATTTATATATATATATAT-TTACTTTT
3934040 TATTATTAGTTTTATTAATTTATATATATATATATTTACTTTT
1 TATTATTA-TTTTATTAATTTATATATATATATATTTACTTTT
* *
3934083 T-TTATT-TTTT-TTATTTTATATATATATTATTTTTACTTTTT
1 TATTATTATTTTATTAATTTATATATATA-TATATTTAC-TTTT
*
3934124 TATTATTATTTTATTTATTT
1 TATTATTATTTTATTAATTT
3934144 GTTTTATTTC
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
39 15 0.17
40 12 0.13
41 5 0.06
42 10 0.11
43 20 0.22
44 27 0.30
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (42 bp):
TATTATTATTTTATTAATTTATATATATATATATTTACTTTT
Found at i:3934091 original size:9 final size:9
Alignment explanation
Indices: 3934074--3934196 Score: 68
Period size: 9 Copynumber: 12.7 Consensus size: 9
3934064 TATATATATA
*
3934074 TTTACTTTT
1 TTTATTTTT
3934083 TTTATTTTT
1 TTTATTTTT
3934092 TTTATTTTAT
1 TTTATTTT-T
*
3934102 ATATATATTATT
1 -T-T-TATTTTT
3934114 TTTACTTTTT
1 TTTA-TTTTT
3934124 TATTATTATTTT
1 T-TTA-T-TTTT
*
3934136 ATTTATTTGT
1 -TTTATTTTT
*
3934146 TTTA-TTTC
1 TTTATTTTT
* *
3934154 TATATTTTA
1 TTTATTTTT
*
3934163 TTTCTTTTT
1 TTTATTTTT
*
3934172 TTTCTTTTT
1 TTTATTTTT
3934181 CTTTATTTTT
1 -TTTATTTTT
*
3934191 TATATT
1 TTTATT
3934197 ACTTACTATT
Statistics
Matches: 90, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
8 5 0.06
9 45 0.50
10 18 0.20
11 7 0.08
12 9 0.10
13 6 0.07
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTATTTTT
Found at i:3934101 original size:39 final size:40
Alignment explanation
Indices: 3933999--3934139 Score: 146
Period size: 39 Copynumber: 3.5 Consensus size: 40
3933989 TTAGTATATA
** * *
3933999 TTTTTA-T-TTTTTTAGATTATATATATAAATATATTATTT
1 TTTTTATTATTTTTTATTTTATATATATATATAT-TTACTT
*
3934038 TTTATTATTAGTTTTATTAATTTATATATATATATATTTACTT
1 TTT-TTATTA-TTTT-TTATTTTATATATATATATATTTACTT
*
3934081 TTTTTATT-TTTTTTATTTTATATATATATTATTTTTAC-T
1 TTTTTATTATTTTTTATTTTATATATATA-TATATTTACTT
3934120 TTTTTATTATTATTTTATTT
1 TTTTTATTATT-TTTTATTT
3934140 ATTTGTTTTA
Statistics
Matches: 88, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
39 27 0.31
40 17 0.19
41 9 0.10
42 5 0.06
43 12 0.14
44 18 0.20
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (40 bp):
TTTTTATTATTTTTTATTTTATATATATATATATTTACTT
Found at i:3934116 original size:31 final size:33
Alignment explanation
Indices: 3934068--3934130 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
3934058 TTTATATATA
*
3934068 TATATATTTACTTTTTTTA-TTTTTT-TTATTT
1 TATATATATACTTTTTTTACTTTTTTATTATTT
3934099 TATATATATA-TTATTTTTACTTTTTTATTATT
1 TATATATATACTT-TTTTTACTTTTTTATTATT
3934131 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 15 0.54
32 6 0.21
33 5 0.18
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (33 bp):
TATATATATACTTTTTTTACTTTTTTATTATTT
Found at i:3934124 original size:25 final size:24
Alignment explanation
Indices: 3934096--3934172 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
3934086 ATTTTTTTTA
3934096 TTTTATATATATATTATT-TTTACTT
1 TTTTAT-TATATATT-TTATTTACTT
*
3934121 TTTTATTAT-TATTTTATTTATTT
1 TTTTATTATATATTTTATTTACTT
*
3934144 GTTTTATTTCTATATTTTATTT-CTT
1 -TTTTA-TTATATATTTTATTTACTT
3934169 TTTT
1 TTTT
3934173 TTCTTTTTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.04
23 10 0.22
24 12 0.27
25 11 0.24
26 10 0.22
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTTATTATATATTTTATTTACTT
Found at i:3934174 original size:13 final size:13
Alignment explanation
Indices: 3934129--3934189 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
3934119 TTTTTTATTA
*
3934129 TTATTTTATTTAT
1 TTATTTTATTTCT
*
3934142 TTGTTTTATTTCT
1 TTATTTTATTTCT
*
3934155 ATATTTTATTTCTT
1 TTATTTTATTTC-T
* *
3934169 TTTTTTCTTTTTCT
1 TTATTT-TATTTCT
3934183 TTATTTT
1 TTATTTT
3934190 TTATATTACT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 22 0.58
14 11 0.29
15 5 0.13
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTCT
Found at i:3934174 original size:83 final size:82
Alignment explanation
Indices: 3934000--3934174 Score: 185
Period size: 83 Copynumber: 2.1 Consensus size: 82
3933990 TAGTATATAT
3934000 TTTTATTTTTTTAGATTATATATATAAATATATTATTTTTTATTATTAGTTTTATTAATTTATAT
1 TTTT-TTTTTTTAGATTATATATATAAATATATTATTTTTTATTATTAGTTTTATTAATTTATAT
*
3934065 ATATATATATTTACTTTT
65 ATATATATATTTACTTTC
** * * * *
3934083 TTTATTTTTTTTATTTTATATATAT-ATTATTTTTACTTTTTTATTATTA-TTTTATTTATTTGT
1 TTT-TTTTTTTTAGATTATATATATAAATA-TATTA-TTTTTTATTATTAGTTTTATTAATTT-A
* * *
3934146 TTTATTTCTATATTTTA-TTTC
62 TATATATATATA-TTTACTTTC
3934167 TTTTTTTT
1 TTTTTTTT
3934175 CTTTTTCTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
82 3 0.04
83 41 0.53
84 29 0.38
85 4 0.05
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (82 bp):
TTTTTTTTTTTAGATTATATATATAAATATATTATTTTTTATTATTAGTTTTATTAATTTATATA
TATATATATTTACTTTC
Found at i:3934186 original size:45 final size:45
Alignment explanation
Indices: 3934132--3934237 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
3934122 TTTATTATTA
* * *
3934132 TTTTATTTATTTGTTT-TATTTC-TA-TATTTTATTTCTTTTTTTTCT
1 TTTTCTTTATTT-TTTATATTACTTACTATTTTA--TCTTTGTTTTCT
3934177 TTTTCTTTATTTTTTATATTACTTACTATTTTATCTTTGTTTTCT
1 TTTTCTTTATTTTTTATATTACTTACTATTTTATCTTTGTTTTCT
* *
3934222 TTATC-TTATCTTTTAT
1 TTTTCTTTATTTTTTAT
3934238 TTAATTTGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 13 0.25
45 31 0.58
46 2 0.04
47 7 0.13
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (45 bp):
TTTTCTTTATTTTTTATATTACTTACTATTTTATCTTTGTTTTCT
Found at i:3934302 original size:15 final size:15
Alignment explanation
Indices: 3934284--3934313 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3934274 TATTTATTTC
3934284 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3934299 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3934314 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:3937899 original size:16 final size:16
Alignment explanation
Indices: 3937873--3937906 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3937863 AGATCCAATC
3937873 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
3937888 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
3937905 AA
1 AA
3937907 AAAACACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:3937921 original size:23 final size:23
Alignment explanation
Indices: 3937895--3937969 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
3937885 GAAAAGAAGC
3937895 AAAAAAGCAAA-AAAAACACAAA-G
1 AAAAAAG-AAACAAAAACA-AAAGG
*
3937918 AAAAAGAGAAACAAGAACAAAAGG
1 AAAAA-AGAAACAAAAACAAAAGG
* *
3937942 AAAAAAG-AGCAAAAATCAAAAAG
1 AAAAAAGAAACAAAAA-CAAAAGG
3937965 AAAAA
1 AAAAA
3937970 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.14
23 24 0.55
24 14 0.32
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAACAAAAACAAAAGG
Found at i:3938609 original size:22 final size:22
Alignment explanation
Indices: 3938581--3938631 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3938571 CCCCATCAAT
3938581 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
3938603 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
3938625 CCTTTGA
1 CCTTTGA
3938632 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:3940097 original size:19 final size:21
Alignment explanation
Indices: 3940073--3940124 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3940063 CGGCCAAGAG
*
3940073 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
3940092 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
3940113 CATGTATTTTCA
1 CATGTATTTTCA
3940125 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:3940872 original size:38 final size:34
Alignment explanation
Indices: 3940827--3940907 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
3940817 ATTGGAGTAC
*
3940827 AAAAAGAAAGAAAAGACAAAAAGAAGAAGAAAATTCA
1 AAAAAGAAAGAAAA-A-AAAAAGAAAAAG-AAATTCA
*
3940864 GAAAAAGAAA-AAAAAGAAAAGAAAAAGAAATTCA
1 -AAAAAGAAAGAAAAAAAAAAGAAAAAGAAATTCA
3940898 AAAAAGAAAG
1 AAAAAGAAAG
3940908 CAAGCCAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 9 0.22
34 7 0.17
35 10 0.25
36 1 0.03
37 4 0.10
38 9 0.22
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (34 bp):
AAAAAGAAAGAAAAAAAAAAGAAAAAGAAATTCA
Found at i:3944206 original size:19 final size:21
Alignment explanation
Indices: 3944182--3944233 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3944172 CGGCCAAGAG
*
3944182 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
3944201 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
3944222 CATGTATTTTCA
1 CATGTATTTTCA
3944234 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:3945479 original size:37 final size:37
Alignment explanation
Indices: 3945388--3945494 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
3945378 CTCACCATTG
3945388 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACTTTA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAACTTTA
* *
3945424 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAACTTTA
* *
3945461 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
3945495 ATTGAAAACA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 28 0.44
37 33 0.52
38 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (37 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAACTTTA
Found at i:3945572 original size:37 final size:35
Alignment explanation
Indices: 3945384--3945489 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 35
3945374 CGTGCTCACC
* *
3945384 ATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTGTCTCCCTTGAGACAATTTCCCTTGAAACAAA
* * * *
3945419 CTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 -ATTGTCTCCCTTGAGACAATTTCCCTTGAAACAAA
* * *
3945455 ATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 A--TTGTCTCCCTTGAGACAATTTCCCTTGAAACA
3945490 TAAACATTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (35 bp):
ATTGTCTCCCTTGAGACAATTTCCCTTGAAACAAA
Found at i:3945580 original size:100 final size:100
Alignment explanation
Indices: 3945403--3945785 Score: 505
Period size: 100 Copynumber: 3.9 Consensus size: 100
3945393 CTTGAGACAG
* * * *
3945403 TTTCCCTTGAAACAAACTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3945468 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
64 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
3945505 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
1 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
*
3945570 AGACAATTTCTCTTGAAACATAAACATTGAAAACA
66 AGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
3945605 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTT
1 TTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
3945669 TGAGACAGTTTCTATTGAAACATAAACTTTGAAAACA
64 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * * * * *
3945706 GTTTCCCTTGAAACAAA----ATCT-TTGA-ATATGTTTTACATT-AAAC-AAATTTCGTCTCTC
1 -TTTCCCTTGAAATAAATTGTCTCTCTTGAGATA-G-TTTCCCTTGAAACAAAATTTTGTCTCCC
3945763 TTGAGACAGTTTCTCTTGAAACA
63 TTGAGACAGTTTCTCTTGAAACA
3945786 AATTTTGTCT
Statistics
Matches: 257, Mismatches: 19, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
94 3 0.01
95 42 0.16
96 9 0.04
100 93 0.36
101 52 0.20
102 58 0.23
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (100 bp):
TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
AGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:3945652 original size:36 final size:36
Alignment explanation
Indices: 3945605--3945690 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
3945595 ATTGAAAACA
** *
3945605 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
3945641 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
3945677 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
3945691 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:3945708 original size:30 final size:30
Alignment explanation
Indices: 3945673--3945731 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3945663 CTCCTTTGAG
*
3945673 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
3945703 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
3945732 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:3945859 original size:37 final size:36
Alignment explanation
Indices: 3945745--3945859 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
3945735 GTTTTACATT
*
3945745 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
3945781 AAACAAATTTTGTCTATCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
3945818 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
3945855 AAACA
1 AAACA
3945860 TCAATCCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 24 0.36
37 24 0.36
38 19 0.28
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:3945964 original size:33 final size:33
Alignment explanation
Indices: 3945900--3946014 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
3945890 CCTTGATACA
3945900 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
3945936 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
3945969 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
3946000 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
3946015 AATTTTGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 3 0.04
36 16 0.21
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:3946061 original size:67 final size:67
Alignment explanation
Indices: 3945969--3946161 Score: 251
Period size: 67 Copynumber: 2.8 Consensus size: 67
3945959 CTTTGAAAAT
*
3945969 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
3946034 CA
66 CA
* * * *
3946036 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAG
* *
3946101 GCC
65 ACA
* * * * *
3946104 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATTTTGTCT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT
3946162 TTTTTAAGAC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 40 0.37
68 33 0.31
69 13 0.12
70 21 0.20
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
CA
Found at i:3946856 original size:105 final size:101
Alignment explanation
Indices: 3946733--3947125 Score: 350
Period size: 105 Copynumber: 3.8 Consensus size: 101
3946723 CGATTTCAAC
* *
3946733 TCCACGATGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
1 TCCACGACGGAGGATAT--TG-GACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
* *
3946798 TGGTTGTCAACGAACAACTTTCCAATTTCAAAGCTGATTT
63 TGGTTGTCAACAAACAA-TTTCCAATTTCAAAGCTAATTT
* *
3946838 TCCACGACGGAGGATATCATGCTAC-CTATGACAACACAAGTTCAACTTCACAACGAAGGGACGG
1 TCCACGACGGAGGATAT--TG-GACTC-AAGACAACACAAGTTCAACTTCACAACGAAGGGACGG
* * ** *
3946902 CTGGTTGTCAAC-AATAATTTCCCAGTTTCAGGGCCAATTT
62 CTGGTTGTCAACAAACAATTT-CCAATTTCAAAGCTAATTT
* * * * * *
3946942 CAACTTCAC-AGCGGAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCG
1 ----TCCACGA-CGGAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACG
** ** * * * *
3947006 GCTGACTGTCAACAAACAATTTCGGA--GCCAATCTCAA-CT
61 GCTGGTTGTCAACAAACAATTTCCAATTTCAAAGCT-AATTT
* * *
3947045 T-CACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
1 TCCACGACGGAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
3947109 TTGTCAACAAACAATTT
66 TTGTCAACAAACAATTT
3947126 TCCGGTTCCA
Statistics
Matches: 239, Mismatches: 38, Indels: 29
0.78 0.12 0.09
Matches are distributed among these distances:
98 69 0.29
99 2 0.01
103 6 0.03
104 21 0.09
105 116 0.49
106 10 0.04
107 1 0.00
108 14 0.06
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (101 bp):
TCCACGACGGAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
TTGTCAACAAACAATTTCCAATTTCAAAGCTAATTT
Found at i:3947079 original size:98 final size:98
Alignment explanation
Indices: 3946867--3947125 Score: 331
Period size: 98 Copynumber: 2.6 Consensus size: 98
3946857 TGCTACCTAT
*
3946867 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCA
1 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-A-AA-----CAATTTCA
* * *
3946932 GGGCCAATTTCAACTTCACAGCGGAGGATATTGGACCCAA
59 GGGCCAATCTCAACTTCACAACGAAGGATATTGGACCCAA
* * * * **
3946972 GACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTC-GGAGCCA
1 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCAGG-GCCA
* *
3947036 ATCTCAACTTCACAACGAAGGATATTGGACTCGA
65 ATCTCAACTTCACAACGAAGGATATTGGACCCAA
3947070 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT
1 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT
3947126 TCCGGTTCCA
Statistics
Matches: 135, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
97 2 0.01
98 89 0.66
103 2 0.01
104 1 0.01
105 41 0.30
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (98 bp):
GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCAGGGCCAA
TCTCAACTTCACAACGAAGGATATTGGACCCAA
Found at i:3947764 original size:34 final size:34
Alignment explanation
Indices: 3947721--3947845 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
3947711 TTCGTCCTAC
*
3947721 TAGGATTCAAACTCCTAAAAATGGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
3947755 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
3947790 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
3947819 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
3947846 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 38 0.52
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:3948144 original size:22 final size:21
Alignment explanation
Indices: 3948114--3948174 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
3948104 CTTTTCTTTT
3948114 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
3948136 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
3948159 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
3948175 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
22 7 0.22
23 12 0.38
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:3948171 original size:24 final size:23
Alignment explanation
Indices: 3948128--3948173 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3948118 CATGTAATAT
*
3948128 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
3948151 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
3948174 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:3948261 original size:9 final size:9
Alignment explanation
Indices: 3948244--3948365 Score: 59
Period size: 9 Copynumber: 12.7 Consensus size: 9
3948234 TATATATATA
*
3948244 TTTACTTTT
1 TTTATTTTT
3948253 TTTATTTTT
1 TTTATTTTT
3948262 TTTATTTTAT
1 TTTATTTT-T
*
3948272 ATATATATTATT
1 -T-T-TATTTTT
3948284 TTTACTTTTT
1 TTTA-TTTTT
3948294 TATTATTATTT
1 T-TTATT-TTT
*
3948305 TATATATTTGT
1 T-T-TATTTTT
*
3948316 TTTA-TTTC
1 TTTATTTTT
*
3948324 TATATTTTT
1 TTTATTTTT
**
3948333 TTCCTTTTT
1 TTTATTTTT
*
3948342 TTCT-TTTTC
1 TT-TATTTTT
3948351 TTTATTTTT
1 TTTATTTTT
*
3948360 TATATT
1 TTTATT
3948366 ACTTACTATT
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.07
9 46 0.53
10 10 0.11
11 14 0.16
12 6 0.07
13 5 0.06
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:3948265 original size:40 final size:40
Alignment explanation
Indices: 3948170--3948312 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 40
3948160 TTAGTATATA
* * *
3948170 TTTTTATTTTTTTTA-GATTATATATATAAATATATTATTT
1 TTTTTATTTTTTTTATTATTATATATATATATAT-TTACTT
***
3948210 TTTATTATCAGTTTTATTAATT-TATATATATATATTTACTT
1 TTT-TTATTTTTTTTATT-ATTATATATATATATATTTACTT
*
3948251 TTTTTATTTTTTTTATT-TTATATATATATTATTTTTAC-T
1 TTTTTATTTTTTTTATTATTATATATATA-TATATTTACTT
3948290 TTTTTATTATTATTTTATATATT
1 TTTTTATT-TT-TTTTAT-TATT
3948313 TGTTTTATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
38 2 0.02
39 17 0.20
40 24 0.29
41 23 0.27
42 13 0.15
43 5 0.06
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (40 bp):
TTTTTATTTTTTTTATTATTATATATATATATATTTACTT
Found at i:3948273 original size:31 final size:34
Alignment explanation
Indices: 3948238--3948311 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 34
3948228 AATTTATATA
*
3948238 TATATATTTACTT-TTTTTA-TTTTTT-TTATT-T
1 TATATATATA-TTATTTTTACTTTTTTATTATTAT
3948269 TATATATATATTATTTTTACTTTTTTATTATTAT
1 TATATATATATTATTTTTACTTTTTTATTATTAT
*
3948303 TTTATATAT
1 TATATATAT
3948312 TTGTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.05
31 15 0.41
32 6 0.16
33 5 0.14
34 9 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (34 bp):
TATATATATATTATTTTTACTTTTTTATTATTAT
Found at i:3948471 original size:15 final size:15
Alignment explanation
Indices: 3948453--3948482 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3948443 TATTTATTTC
3948453 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3948468 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3948483 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:3951078 original size:19 final size:20
Alignment explanation
Indices: 3951054--3951093 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
3951044 TATCCTTTCT
3951054 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
3951073 TTATTTCATTTCATTACTTA
1 TTATTTCATTTCATTACTTA
3951093 T
1 T
3951094 ATTATTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:3951401 original size:19 final size:17
Alignment explanation
Indices: 3951362--3951410 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3951352 TTAGAGTACA
*
3951362 AAAAGAAAGAAAAAGAC
1 AAAAGAAAGAAAAACAC
*
3951379 AAAAGAAGAGAAAAATCAG
1 AAAAGAA-AGAAAAA-CAC
3951398 AAAAGAAAAGAAA
1 AAAAG-AAAGAAA
3951411 TTCAAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 11 0.41
20 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAAAACAC
Found at i:3958919 original size:10 final size:11
Alignment explanation
Indices: 3958898--3958922 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3958888 ACGCACAACG
3958898 AAAATACAAAA
1 AAAATACAAAA
3958909 AAAATACAAAA
1 AAAATACAAAA
3958920 AAA
1 AAA
3958923 GTGCAACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAATACAAAA
Found at i:3977752 original size:12 final size:12
Alignment explanation
Indices: 3977737--3977776 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3977727 AAATTTTGGC
3977737 TTTTTTGGTTTT
1 TTTTTTGGTTTT
3977749 TTTTTT-G--TT
1 TTTTTTGGTTTT
*
3977758 TTTTTTGTTTTT
1 TTTTTTGGTTTT
3977770 TTTTTTG
1 TTTTTTG
3977777 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
9 8 0.33
11 1 0.04
12 15 0.62
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTTTGGTTTT
Found at i:3977753 original size:20 final size:20
Alignment explanation
Indices: 3977730--3977773 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3977720 TTTTTTGAAA
3977730 TTTTGGCTTTTTTGGTTTTT
1 TTTTGGCTTTTTTGGTTTTT
* * *
3977750 TTTTTGTTTTTTTTGTTTTT
1 TTTTGGCTTTTTTGGTTTTT
3977770 TTTT
1 TTTT
3977774 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (20 bp):
TTTTGGCTTTTTTGGTTTTT
Found at i:3977754 original size:21 final size:21
Alignment explanation
Indices: 3977730--3977776 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3977720 TTTTTTGAAA
3977730 TTTTGGCTTTTTTGGTTTTTT
1 TTTTGGCTTTTTTGGTTTTTT
** *
3977751 TTTTGTTTTTTTTGTTTTTTT
1 TTTTGGCTTTTTTGGTTTTTT
3977772 TTTTG
1 TTTTG
3977777 AAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (21 bp):
TTTTGGCTTTTTTGGTTTTTT
Found at i:3977772 original size:9 final size:9
Alignment explanation
Indices: 3977747--3977772 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3977737 TTTTTTGGTT
3977747 TTTTTTTTG
1 TTTTTTTTG
3977756 TTTTTTTTG
1 TTTTTTTTG
3977765 TTTTTTTT
1 TTTTTTTT
3977773 TTTGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3977774 original size:20 final size:20
Alignment explanation
Indices: 3977737--3977774 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3977727 AAATTTTGGC
3977737 TTTTTTGGTTTTTTTTTTGT
1 TTTTTTGGTTTTTTTTTTGT
*
3977757 TTTTTTTGTTTTTTTTTT
1 TTTTTTGGTTTTTTTTTT
3977775 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (20 bp):
TTTTTTGGTTTTTTTTTTGT
Found at i:3979735 original size:13 final size:11
Alignment explanation
Indices: 3979694--3979778 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
3979684 ACAATCTGTC
3979694 CATCACCATTAT
1 CATCACCA-TAT
*
3979706 CA-CGCCTATAT
1 CATCACC-ATAT
3979717 CATCACCATAGT
1 CATCACCATA-T
3979729 CCATCACCATTAT
1 -CATCACCA-TAT
*
3979742 CA-CGCCTATAT
1 CATCACC-ATAT
3979753 CATCACCATATT
1 CATCACCATA-T
3979765 CCATCACCATAT
1 -CATCACCATAT
3979777 CA
1 CA
3979779 CGCCTACATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3979738 original size:36 final size:36
Alignment explanation
Indices: 3979691--3979795 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
3979681 GATACAATCT
3979691 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
3979727 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
3979763 TTCCATCACCA-TATCACGCCTACATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
3979796 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:3980259 original size:9 final size:9
Alignment explanation
Indices: 3980245--3980288 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
3980235 TTTGGAGTGC
*
3980245 AAAAGAAAG
1 AAAAGAAAA
3980254 AAAAGAAAA
1 AAAAGAAAA
3980263 AAAAGAATAA
1 AAAAGAA-AA
3980273 AAAAGCAAAGA
1 AAAAG-AAA-A
3980284 AAAAG
1 AAAAG
3980289 TGAAGCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 15 0.48
10 8 0.26
11 8 0.26
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:3983914 original size:13 final size:11
Alignment explanation
Indices: 3983892--3983957 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
3983882 TATCACGCCT
3983892 ATATCATCACC
1 ATATCATCACC
3983903 ATAGTCCATCACC
1 ATA-T-CATCACC
*
3983916 ATTATCA-CGCC
1 A-TATCATCACC
3983927 TATATCATCACC
1 -ATATCATCACC
3983939 ATATTCCATCACC
1 ATA-T-CATCACC
3983952 ATATCA
1 ATATCA
3983958 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:3983922 original size:36 final size:36
Alignment explanation
Indices: 3983870--3983974 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
3983860 GATACAATAT
*
3983870 GTCCCTCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
3983906 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
3983942 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
3983975 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:4005263 original size:16 final size:15
Alignment explanation
Indices: 4005241--4005279 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4005231 TTGGCTTTTT
4005241 TTTTGTTTTTTTGCC
1 TTTTGTTTTTTTGCC
4005256 TCTTTG-TTTTTTGCC
1 T-TTTGTTTTTTTGCC
4005271 TTTT-TTTTT
1 TTTTGTTTTT
4005280 GTTTTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.32
15 11 0.50
16 4 0.18
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (15 bp):
TTTTGTTTTTTTGCC
Found at i:4005265 original size:21 final size:21
Alignment explanation
Indices: 4005220--4005265 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
4005210 TTTTTTGAAA
*
4005220 TTTTGGTTTTTTTGGCTTTT-
1 TTTTGGTTTTTTTGCCTTTTG
*
4005240 TTTTTGTTTTTTTGCCTCTTTG
1 TTTTGGTTTTTTTGCCT-TTTG
4005262 TTTT
1 TTTT
4005266 TTGCCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 3 0.14
22 4 0.18
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (21 bp):
TTTTGGTTTTTTTGCCTTTTG
Found at i:4006638 original size:19 final size:20
Alignment explanation
Indices: 4006591--4006641 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4006581 AAAACCCCTT
**
4006591 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
4006611 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4006630 TGAAGATACATG
1 TGAAAATACATG
4006642 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4007316 original size:35 final size:36
Alignment explanation
Indices: 4007270--4007357 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
4007260 AGAAATGGAA
*
4007270 ATGGAATATGGTGATGATATATGCGTGAT-ATGATG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGATG
* * *
4007305 ATGGACTATGGTGAAGATATAGGCGTGATAATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGATG
*
4007341 ATGGAAGATGGTGATGA
1 ATGGAATATGGTGATGA
4007358 GCAGATTGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 26 0.58
36 19 0.42
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (36 bp):
ATGGAATATGGTGATGATATAGGCGTGATAATGATG
Found at i:4010599 original size:15 final size:16
Alignment explanation
Indices: 4010548--4010600 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
4010538 AAGTAATGAA
4010548 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
4010565 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
4010582 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
4010597 ATAA
1 ATAA
4010601 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:4011265 original size:35 final size:36
Alignment explanation
Indices: 4011226--4011305 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
4011216 AAATGGAATT
**
4011226 TGGTGATGATATAGGCGTGAT-ATGATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
* *
4011261 TGGTGAAGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
4011297 TGGTGATGA
1 TGGTGATGA
4011306 ACAGATTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 20 0.51
36 19 0.49
ACGTcount: A:0.30, C:0.04, G:0.38, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGATGATGGAAGA
Found at i:4014547 original size:15 final size:16
Alignment explanation
Indices: 4014496--4014548 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
4014486 AAGTAATGAA
4014496 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
4014513 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
4014530 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
4014545 ATAA
1 ATAA
4014549 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:4015214 original size:35 final size:36
Alignment explanation
Indices: 4015175--4015254 Score: 108
Period size: 35 Copynumber: 2.2 Consensus size: 36
4015165 AAATGGAATT
* **
4015175 TGGTGATGATATAGGCGTGAT-ATGATGATGGACTA
1 TGGTGATGATATAGGCGTGATAAAGATGATGGAAGA
* *
4015210 TGGTGATGATATAGGTGTGATAAAGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAAAGATGATGGAAGA
4015246 TGGTGATGA
1 TGGTGATGA
4015255 ACAGATTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 20 0.51
36 19 0.49
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAAAGATGATGGAAGA
Found at i:4022978 original size:12 final size:12
Alignment explanation
Indices: 4022961--4022989 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4022951 GAAAAGCAAC
4022961 AACTGTGGAAGA
1 AACTGTGGAAGA
4022973 AACTGTGGAAGA
1 AACTGTGGAAGA
4022985 AACTG
1 AACTG
4022990 ATCCAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.17
Consensus pattern (12 bp):
AACTGTGGAAGA
Found at i:4028800 original size:28 final size:26
Alignment explanation
Indices: 4028769--4028825 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
4028759 GAAAATCAGA
* *
4028769 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACT-CAAAAG-AAG
*
4028797 AAAGAAAATCCAGCACTCAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAGAAG
4028823 AAA
1 AAA
4028826 AAGCAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 14 0.54
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAGAAAATCAAGCACTCAAAAGAAG
Found at i:4033982 original size:31 final size:31
Alignment explanation
Indices: 4033919--4033982 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4033909 AATGGTTAAA
* *
4033919 AAAGAATACGGTAATGAAATAAGAAAAGATG
1 AAAGAATAAGGTAATGAAATAAGAAAAAATG
4033950 AAAGAATAAGG-AGATGAAAT-AGTAAAAAATG
1 AAAGAATAAGGTA-ATGAAATAAG-AAAAAATG
4033981 AA
1 AA
4033983 GATAACTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.61, C:0.02, G:0.22, T:0.16
Consensus pattern (31 bp):
AAAGAATAAGGTAATGAAATAAGAAAAAATG
Found at i:4034197 original size:13 final size:13
Alignment explanation
Indices: 4034175--4034206 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4034165 GATATATGAG
4034175 TCTT-TTTCTTTT
1 TCTTCTTTCTTTT
4034187 TCTTCTTTCTTTT
1 TCTTCTTTCTTTT
4034200 TC-TCTTT
1 TCTTCTTT
4034207 TTGTTGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTCTTTCTTTT
Found at i:4034444 original size:32 final size:33
Alignment explanation
Indices: 4034383--4034449 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
4034373 CAAAAATTAA
*
4034383 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAAAGGAATATGGATAG
4034415 AAGAAAGGAAATGA-TAAGAAAGGAA-ATGGATAG
1 AAGAAA-GAAATGATTAA-AAAGGAATATGGATAG
4034448 AA
1 AA
4034450 ATGTTATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAAAGGAATATGGATAG
Found at i:4034626 original size:35 final size:35
Alignment explanation
Indices: 4034587--4034663 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
4034577 TGGTAAAGGA
* * *
4034587 ATGGTGGTTATATAGGTGTGAAATGGTGATAGAAC
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAC
* * * *
4034622 ATGGTAATGATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAC
4034657 ATGGTGA
1 ATGGTGA
4034664 AGAATAGATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAC
Found at i:4039589 original size:14 final size:11
Alignment explanation
Indices: 4039546--4039578 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
4039536 TAACATTGGT
4039546 TCTTCTTTGAG
1 TCTTCTTTGAG
4039557 TCTTCTTTGAG
1 TCTTCTTTGAG
4039568 TCTTCTTTGAG
1 TCTTCTTTGAG
4039579 ATACTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.55
Consensus pattern (11 bp):
TCTTCTTTGAG
Found at i:4048769 original size:24 final size:23
Alignment explanation
Indices: 4048737--4048784 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
4048727 GATGTAGGAG
4048737 TCTTTTTCTT-TTCTCTTTTGTTT
1 TCTTTTTCTTGTT-TCTTTTGTTT
*
4048760 TCTTCTTTCTTGTTTCTTTTTTTT
1 TCTT-TTTCTTGTTTCTTTTGTTT
4048784 T
1 T
4048785 TGTTGTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 16 0.73
25 2 0.09
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (23 bp):
TCTTTTTCTTGTTTCTTTTGTTT
Found at i:4052714 original size:13 final size:13
Alignment explanation
Indices: 4052692--4052721 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4052682 ACTAAACACC
4052692 TTTC-ACATACCT
1 TTTCAACATACCT
4052704 TTTCAACATACCT
1 TTTCAACATACCT
4052717 TTTCA
1 TTTCA
4052722 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:4062279 original size:13 final size:13
Alignment explanation
Indices: 4062257--4062286 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4062247 ACTAAACACC
4062257 TTTC-ACATACCT
1 TTTCAACATACCT
4062269 TTTCAACATACCT
1 TTTCAACATACCT
4062282 TTTCA
1 TTTCA
4062287 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:4065061 original size:28 final size:28
Alignment explanation
Indices: 4065030--4065090 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
4065020 CTTTTCTTTG
*
4065030 CTTTTTCTTCTTTT-GAGTGCTGGAATTT
1 CTTTTT-TTCTTTTGGAGTGCTGCAATTT
* * *
4065058 CTTTCTTTCTTTTGGAGTGTTTCAATTT
1 CTTTTTTTCTTTTGGAGTGCTGCAATTT
4065086 CTTTT
1 CTTTT
4065091 CTGATTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.10, C:0.15, G:0.15, T:0.61
Consensus pattern (28 bp):
CTTTTTTTCTTTTGGAGTGCTGCAATTT
Found at i:4072302 original size:11 final size:11
Alignment explanation
Indices: 4072288--4072314 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4072278 TCAAAAAAAC
4072288 AAAAAAAGCCA
1 AAAAAAAGCCA
4072299 AAAAAAAGCCA
1 AAAAAAAGCCA
4072310 AAAAA
1 AAAAA
4072315 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCCA
Found at i:4072305 original size:20 final size:20
Alignment explanation
Indices: 4072280--4072321 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4072270 TTTTTTAATC
4072280 AAAAAAACAAAAAAAGCCAA
1 AAAAAAACAAAAAAAGCCAA
* *
4072300 AAAAAAGCCAAAAAAGCCAA
1 AAAAAAACAAAAAAAGCCAA
4072320 AA
1 AA
4072322 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAGCCAA
Found at i:4072312 original size:9 final size:9
Alignment explanation
Indices: 4072279--4072321 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
4072269 TTTTTTTAAT
*
4072279 CAAAAAAAC
1 CAAAAAAGC
*
4072288 AAAAAAAGC
1 CAAAAAAGC
4072297 CAAAAAAAAGC
1 C--AAAAAAGC
4072308 CAAAAAAGC
1 CAAAAAAGC
4072317 CAAAA
1 CAAAA
4072322 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 20 0.69
11 9 0.31
ACGTcount: A:0.74, C:0.19, G:0.07, T:0.00
Consensus pattern (9 bp):
CAAAAAAGC
Found at i:4077324 original size:19 final size:20
Alignment explanation
Indices: 4077283--4077333 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4077273 GAAACCCCTT
*
4077283 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
4077303 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4077322 TGAAGATACATG
1 TGAAAATACATG
4077334 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4078283 original size:30 final size:30
Alignment explanation
Indices: 4078248--4078304 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4078238 CTGCCATGAT
**
4078248 ATCTAAATGAAATGAAAACATAATATATTA
1 ATCTAAAACAAATGAAAACATAATATATTA
* *
4078278 ATCTAAAACATATGTAAACATAATATA
1 ATCTAAAACAAATGAAAACATAATATA
4078305 AAGCTAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (30 bp):
ATCTAAAACAAATGAAAACATAATATATTA
Found at i:4081513 original size:19 final size:20
Alignment explanation
Indices: 4081472--4081522 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4081462 GAAACCCCTT
*
4081472 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
4081492 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4081511 TGAAGATACATG
1 TGAAAATACATG
4081523 CTCTTGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4085661 original size:16 final size:16
Alignment explanation
Indices: 4085640--4085671 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4085630 TCTTCCACCA
4085640 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
4085656 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
4085672 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:4087781 original size:5 final size:5
Alignment explanation
Indices: 4087771--4087836 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
4087761 GAACTTCTCT
* ** *
4087771 TTTTC TTTTC TTTTC CTTTC TTCTTC TTTTC TGAT- TTTTC TCTTC -TTT-
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
4087819 TTGTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTT
4087837 TGCACTCCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
4 10 0.22
5 31 0.67
6 5 0.11
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:4087790 original size:10 final size:10
Alignment explanation
Indices: 4087771--4087836 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 10
4087761 GAACTTCTCT
4087771 TTTTCTTTTC
1 TTTTCTTTTC
*
4087781 TTTTCCTTTC
1 TTTTCTTTTC
4087791 TTCTTCTTTTC
1 TT-TTCTTTTC
**
4087802 TGAT-TTTTC
1 TTTTCTTTTC
*
4087811 TCTTC-TTT-
1 TTTTCTTTTC
*
4087819 TTGTCTTTTC
1 TTTTCTTTTC
4087829 -TTTCTTTT
1 TTTTCTTTT
4087837 TGCACTCCAA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
8 3 0.07
9 20 0.47
10 12 0.28
11 8 0.19
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:4087816 original size:19 final size:18
Alignment explanation
Indices: 4087787--4087838 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 18
4087777 TTTCTTTTCC
4087787 TTTCTTCTTCTTTTCTGAT-T
1 TTTC-TCTTCTTTT-TG-TCT
4087807 TTTCTCTTCTTTTTGTCT
1 TTTCTCTTCTTTTTGTCT
4087825 TTTCT-TTCTTTTTG
1 TTTCTCTTCTTTTTG
4087839 CACTCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.32
18 8 0.26
19 9 0.29
20 4 0.13
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (18 bp):
TTTCTCTTCTTTTTGTCT
Found at i:4089278 original size:16 final size:16
Alignment explanation
Indices: 4089257--4089288 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4089247 TCTTCCACCA
4089257 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
4089273 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
4089289 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:4091396 original size:5 final size:5
Alignment explanation
Indices: 4091386--4091459 Score: 52
Period size: 5 Copynumber: 15.8 Consensus size: 5
4091376 GAACTTCTCT
* **
4091386 TTTTC TTTTC TTTTC CTTTC TTCTTC TTTTC --TTC TTTTC TGAT- TTTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
* *
4091434 TCTTC -TTT- TTGTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
4091460 TGCACTCCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 34 0.65
6 5 0.10
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:4091437 original size:19 final size:18
Alignment explanation
Indices: 4091379--4091461 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
4091369 TCTTTTTGAA
4091379 CTTCTCTTTT-TCTTTTCT
1 CTTCT-TTTTGTCTTTTCT
* * *
4091397 TTTCCTTTCT-TCTTCTTTT
1 CTT-CTTTTTGTCTT-TTCT
4091416 CTTCTTTTCTGAT-TTTTCT
1 CTTCTTTT-TG-TCTTTTCT
4091435 CTTCTTTTTGTCTTTTCT
1 CTTCTTTTTGTCTTTTCT
4091453 -TTCTTTTTG
1 CTTCTTTTTG
4091462 CACTCCAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
17 10 0.19
18 21 0.40
19 19 0.36
20 2 0.04
21 1 0.02
ACGTcount: A:0.01, C:0.23, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTCTTTTTGTCTTTTCT
Found at i:4091458 original size:17 final size:18
Alignment explanation
Indices: 4091410--4091461 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
4091400 CCTTTCTTCT
4091410 TCTTTTC-TTCTTTTCTGA
1 TCTTTTCTTTCTTTT-TGA
4091428 T-TTTTCTCTTCTTTTTG-
1 TCTTTTCT-TTCTTTTTGA
4091445 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCTTTTTG
4091462 CACTCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 15 0.48
18 9 0.29
19 7 0.23
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (18 bp):
TCTTTTCTTTCTTTTTGA
Found at i:4091459 original size:27 final size:27
Alignment explanation
Indices: 4091379--4091459 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 27
4091369 TCTTTTTGAA
*
4091379 CTTCTCTTTTTCTTTTCTTTTCCTTTCTT
1 CTTCT-TTTTTCTTTTC-TTTCTTTTCTT
*
4091408 CTTCTTTTCTTCTTTTCTGAT-TTTTC-T
1 CTTCTTTT-TTCTTTTCT-TTCTTTTCTT
4091435 CTTCTTTTTGTCTTTTCTTTCTTTT
1 CTTCTTTTT-TCTTTTCTTTCTTTT
4091460 TGCACTCCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 2 0.04
27 21 0.47
28 8 0.18
29 14 0.31
ACGTcount: A:0.01, C:0.23, G:0.02, T:0.73
Consensus pattern (27 bp):
CTTCTTTTTTCTTTTCTTTCTTTTCTT
Found at i:4092901 original size:16 final size:16
Alignment explanation
Indices: 4092880--4092911 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4092870 TCTTCCACCA
4092880 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
4092896 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
4092912 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:4094882 original size:19 final size:19
Alignment explanation
Indices: 4094855--4094916 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
4094845 TCTTTTTGAA
*
4094855 TTTTTTTCTTTTTCTTTTC
1 TTTTCTTCTTTTTCTTTTC
4094874 TTTTCTTCTTTTT-TGATTT-
1 TTTTCTTCTTTTTCT--TTTC
*
4094893 TTCTCTTCTTTTGTCTTTTTC
1 TTTTCTTCTTTT-TC-TTTTC
4094914 TTT
1 TTT
4094917 CCTTTTGCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 1 0.03
19 23 0.68
20 7 0.21
21 2 0.06
22 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTCTTCTTTTTCTTTTC
Found at i:4095222 original size:20 final size:20
Alignment explanation
Indices: 4095184--4095224 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4095174 GGGTAATAAT
*
4095184 ATAAGTAATGAAAGGAAATA
1 ATAAGTAATGAAAGAAAATA
4095204 ATAAG-AATGAAATGAAAATA
1 ATAAGTAATGAAA-GAAAATA
4095224 A
1 A
4095225 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAGAAAATA
Found at i:4099475 original size:19 final size:21
Alignment explanation
Indices: 4099432--4099483 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
4099422 GAAACCCCTT
4099432 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
4099453 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4099472 TGAAGATACATG
1 TGAAAATACATG
4099484 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:4111713 original size:19 final size:21
Alignment explanation
Indices: 4111689--4111740 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4111679 CGGCCAAGAG
*
4111689 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
4111708 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
4111729 CATGTATTTTCA
1 CATGTATTTTCA
4111741 AATGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:4112176 original size:19 final size:20
Alignment explanation
Indices: 4112152--4112191 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4112142 TATCATTTCT
4112152 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
4112171 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
4112191 T
1 T
4112192 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:4112194 original size:19 final size:18
Alignment explanation
Indices: 4112148--4112194 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4112138 TCTCTATCAT
4112148 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
4112165 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
4112184 TTACTTATATT
1 TT-CTTATATT
4112195 ATTATTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:4115341 original size:8 final size:8
Alignment explanation
Indices: 4115317--4115369 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
4115307 AATTGGAGTG
4115317 AAAAAAGA
1 AAAAAAGA
4115325 AAGAAAAGA
1 AA-AAAAGA
*
4115334 TAAAAAGA
1 AAAAAAGA
*
4115342 AGAAAA-A
1 AAAAAAGA
*
4115349 AGAAAAGA
1 AAAAAAGA
4115357 AGAAAAAGA
1 A-AAAAAGA
4115366 AAAA
1 AAAA
4115370 GATTTCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
7 7 0.18
8 17 0.45
9 14 0.37
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:4115350 original size:23 final size:21
Alignment explanation
Indices: 4115324--4115369 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
4115314 GTGAAAAAAG
4115324 AAAGAAAAGATAAAAAGAAGAAA
1 AAAGAAAAGA-AAAAA-AAGAAA
*
4115347 AAAGAAAAGAAGAAAAAGAAA
1 AAAGAAAAGAAAAAAAAGAAA
4115368 AA
1 AA
4115370 GATTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAGAAAAGAAAAAAAAGAAA
Found at i:4115364 original size:14 final size:15
Alignment explanation
Indices: 4115316--4115368 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 15
4115306 AAATTGGAGT
4115316 GAAAAAAG-AAAGAA
1 GAAAAAAGAAAAGAA
* *
4115330 -AAGATA-AAAAGAA
1 GAAAAAAGAAAAGAA
4115343 GAAAAAAGAAAAGAA
1 GAAAAAAGAAAAGAA
4115358 G-AAAAAGAAAA
1 GAAAAAAGAAAA
4115369 AGATTTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 10 0.31
14 14 0.44
15 8 0.25
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
GAAAAAAGAAAAGAA
Found at i:4115369 original size:15 final size:14
Alignment explanation
Indices: 4115317--4115371 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 14
4115307 AATTGGAGTG
4115317 AAAAAAGAAAGAAAA
1 AAAAAAG-AAGAAAA
4115332 GATAAAAAGAAGAAAA
1 -A-AAAAAGAAGAAAA
4115348 AAGAAAAGAAGAAAA
1 AA-AAAAGAAGAAAA
4115363 AGAAAAAGA
1 A-AAAAAGA
4115372 TTTCAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.03
15 20 0.56
16 9 0.25
17 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAGAAAA
Found at i:4115371 original size:27 final size:27
Alignment explanation
Indices: 4115316--4115371 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4115306 AAATTGGAGT
* *
4115316 GAAAAAAGAAAGAAAAGATAAAAAGAA
1 GAAAAAAGAAAGAAAAGAAAAAAAAAA
*
4115343 GAAAAAAGAAA-AGAAGAAAAAGAAAAA
1 GAAAAAAGAAAGAAAAGAAAAA-AAAAA
4115370 GA
1 GA
4115372 TTTCAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (27 bp):
GAAAAAAGAAAGAAAAGAAAAAAAAAA
Found at i:4119827 original size:13 final size:12
Alignment explanation
Indices: 4119808--4119893 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
4119798 ATATAGCCGT
4119808 GATATGGTGATG
1 GATATGGTGATG
4119820 GAATATGGTGAT-
1 G-ATATGGTGATG
*
4119832 GATATAGGCG-T-
1 GATAT-GGTGATG
4119843 GATAATGGTGATG
1 GAT-ATGGTGATG
4119856 GACTATGGTGAT-
1 GA-TATGGTGATG
*
4119868 GATATAGGCG-T-
1 GATAT-GGTGATG
4119879 GATAATGGTGATG
1 GAT-ATGGTGATG
4119892 GA
1 GA
4119894 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:4119863 original size:36 final size:36
Alignment explanation
Indices: 4119790--4119894 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
4119780 ATTTATAAGT
* * *
4119790 TGGTGATAATATAGCCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
4119825 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
4119861 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
4119895 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:4123921 original size:7 final size:6
Alignment explanation
Indices: 4123889--4123922 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
4123879 GTTGTAGGAG
*
4123889 TCTTTT TCTTTT TCTTTT TGTTTT TCTTCTT TCT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCT
4123923 CGTTGCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:4124338 original size:13 final size:12
Alignment explanation
Indices: 4124319--4124404 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
4124309 ATATAGGCGT
4124319 GATATGGTGATG
1 GATATGGTGATG
4124331 GAATATGGTGAT-
1 G-ATATGGTGATG
*
4124343 GATATAGGCG-T-
1 GATAT-GGTGATG
4124354 GATAATGGTGATG
1 GAT-ATGGTGATG
4124367 GACTATGGTGAT-
1 GA-TATGGTGATG
*
4124379 GATATAGGCG-T-
1 GATAT-GGTGATG
4124390 GATAATGGTGATG
1 GAT-ATGGTGATG
4124403 GA
1 GA
4124405 AAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:4124374 original size:36 final size:36
Alignment explanation
Indices: 4124301--4124405 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
4124291 ATTTATAAGT
*
4124301 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
4124336 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
4124372 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
4124406 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:4127939 original size:19 final size:20
Alignment explanation
Indices: 4127898--4127948 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4127888 GAAACCCCTT
*
4127898 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
4127918 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4127937 TGAAGATACATG
1 TGAAAATACATG
4127949 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4132338 original size:27 final size:27
Alignment explanation
Indices: 4132299--4132356 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
4132289 TGGTAGTATG
*
4132299 ACAAAAGGTCCATTCATGATTGTTTTC
1 ACAAAAGGGCCATTCATGATTGTTTTC
4132326 ACAAAAGGGCCATTCATGATTGTTTTC
1 ACAAAAGGGCCATTCATGATTGTTTTC
4132353 ACAA
1 ACAA
4132357 TCAATACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (27 bp):
ACAAAAGGGCCATTCATGATTGTTTTC
Found at i:4135650 original size:26 final size:26
Alignment explanation
Indices: 4135607--4135681 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 26
4135597 GTGCTTCAAC
***
4135607 TTCTTTCTTTTCTTTGCTTTGCTTTT
1 TTCTTTCTTTTGAGTGCTTTGCTTTT
**
4135633 CTTCTTT-TTTTGAGTGC--TGGATTT
1 -TTCTTTCTTTTGAGTGCTTTGCTTTT
*
4135657 TTCTTTCTTTTGAGTGCTTTACTTT
1 TTCTTTCTTTTGAGTGCTTTGCTTT
4135682 GCTTTCTGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
23 6 0.16
24 15 0.41
26 10 0.27
27 6 0.16
ACGTcount: A:0.05, C:0.16, G:0.13, T:0.65
Consensus pattern (26 bp):
TTCTTTCTTTTGAGTGCTTTGCTTTT
Found at i:4135686 original size:24 final size:24
Alignment explanation
Indices: 4135636--4135688 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4135626 TGCTTTTCTT
* *
4135636 CTTT-TTTTGAGTGCTGGATTTTT
1 CTTTCTTTTGAGTGCTGGACTTTG
**
4135659 CTTTCTTTTGAGTGCTTTACTTTG
1 CTTTCTTTTGAGTGCTGGACTTTG
4135683 CTTTCT
1 CTTTCT
4135689 GATTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.08, C:0.15, G:0.17, T:0.60
Consensus pattern (24 bp):
CTTTCTTTTGAGTGCTGGACTTTG
Found at i:4136556 original size:26 final size:26
Alignment explanation
Indices: 4136520--4136587 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
4136510 ATGAACCCAC
*
4136520 ATGCAAGGCACATGGGGCCTGGTCAT
1 ATGCAAGGCACATGGGGCCTGATCAT
*
4136546 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAGGCACATGGGGCCTGATCAT
* **
4136572 ATACAAAACACATGGG
1 ATGCAAGGCACATGGG
4136588 TGTTCTAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.18
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGCCTGATCAT
Found at i:4141235 original size:12 final size:12
Alignment explanation
Indices: 4141196--4141245 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4141186 TTGATTTCAC
4141196 TTTTTCTTTTCT
1 TTTTTCTTTTCT
**
4141208 TTCTTTCTTTGAT
1 TT-TTTCTTTTCT
4141221 TTTTTCTTTTCT
1 TTTTTCTTTTCT
*
4141233 TTTTGC-TTTCT
1 TTTTTCTTTTCT
4141244 TT
1 TT
4141246 CTTTTTGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:4141242 original size:16 final size:15
Alignment explanation
Indices: 4141198--4141253 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
4141188 GATTTCACTT
4141198 TTTC-TTTT-CTTTC
1 TTTCTTTTTGCTTTC
*
4141211 TTTCTTTGATT-TTTTC
1 TTTCTTT--TTGCTTTC
4141227 TTTTCTTTTTGCTTTC
1 -TTTCTTTTTGCTTTC
4141243 TTTCTTTTTGC
1 TTTCTTTTTGC
4141254 ACGCTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 4 0.11
14 2 0.06
15 13 0.36
16 10 0.28
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTGCTTTC
Done.